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Conformational and functional characterization of artificially conjugated non-canonical ubiquitin dimers

Conformational and functional characterization of artificially conjugated non-canonical ubiquitin dimers

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SCHNEIDER, Tobias, Andrej BERG, Zeynel ULUSOY, Martin GAMERDINGER, Christine PETER, Michael KOVERMANN, 2019. Conformational and functional characterization of artificially conjugated non-canonical ubiquitin dimers. In: Scientific reports. 9, 19991. eISSN 2045-2322. Available under: doi: 10.1038/s41598-019-56458-z

@article{Schneider2019-12-27Confo-48218, title={Conformational and functional characterization of artificially conjugated non-canonical ubiquitin dimers}, year={2019}, doi={10.1038/s41598-019-56458-z}, volume={9}, journal={Scientific reports}, author={Schneider, Tobias and Berg, Andrej and Ulusoy, Zeynel and Gamerdinger, Martin and Peter, Christine and Kovermann, Michael}, note={Article Number: 19991} }

<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:void="http://rdfs.org/ns/void#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > <rdf:Description rdf:about="https://kops.uni-konstanz.de/rdf/resource/123456789/48218"> <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/48218/3/Schneider_2-x6eyirh6wvii5.pdf"/> <dc:rights>Attribution 4.0 International</dc:rights> <dc:language>eng</dc:language> <dc:creator>Berg, Andrej</dc:creator> <dcterms:title>Conformational and functional characterization of artificially conjugated non-canonical ubiquitin dimers</dcterms:title> <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/rdf/resource/123456789/29"/> <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2020-01-14T11:48:53Z</dc:date> <dcterms:issued>2019-12-27</dcterms:issued> <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/48218/3/Schneider_2-x6eyirh6wvii5.pdf"/> <dc:creator>Gamerdinger, Martin</dc:creator> <dc:contributor>Peter, Christine</dc:contributor> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2020-01-14T11:48:53Z</dcterms:available> <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/48218"/> <dc:creator>Kovermann, Michael</dc:creator> <dcterms:rights rdf:resource="http://creativecommons.org/licenses/by/4.0/"/> <dc:creator>Ulusoy, Zeynel</dc:creator> <foaf:homepage rdf:resource="http://localhost:8080/jspui"/> <dc:creator>Peter, Christine</dc:creator> <dcterms:abstract xml:lang="eng">Ubiquitylation is an eminent posttranslational modification referring to the covalent attachment of single ubiquitin molecules or polyubiquitin chains to a target protein dictating the fate of such labeled polypeptide chains. Here, we have biochemically produced artificially Lys11-, and Lys27-, and Lys63-linked ubiquitin dimers based on click-chemistry generating milligram quantities in high purity. We show that the artificial linkage used for the conjugation of two ubiquitin moieties represents a fully reliable surrogate of the natural isopeptide bond by acquiring highly resolved nuclear magnetic resonance (NMR) spectroscopic data including ligand binding studies. Extensive coarse grained and atomistic molecular dynamics (MD) simulations allow to extract structures representing the ensemble of domain-domain conformations used to verify the experimental data. Advantageously, this methodology does not require individual isotopic labeling of both ubiquitin moieties as NMR data have been acquired on the isotopically labeled proximal moiety and complementary MD simulations have been used to fully interpret the experimental data in terms of domain-domain conformation. This combined approach intertwining NMR spectroscopy with MD simulations makes it possible to describe the conformational space non-canonically Lys11-, and Lys27-linked ubiquitin dimers occupy in a solution averaged ensemble by taking atomically resolved information representing all residues in ubiquitin dimers into account.</dcterms:abstract> <dc:contributor>Gamerdinger, Martin</dc:contributor> <dc:contributor>Kovermann, Michael</dc:contributor> <dc:contributor>Schneider, Tobias</dc:contributor> <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/rdf/resource/123456789/29"/> <dc:creator>Schneider, Tobias</dc:creator> <dc:contributor>Berg, Andrej</dc:contributor> <dc:contributor>Ulusoy, Zeynel</dc:contributor> </rdf:Description> </rdf:RDF>

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